The groundwater table fluctuation zone is the main interface for contaminants to transport between the unsaturated soil and saturated aquifers which still lacks of concern. In this study, we explored the interactions of Cr(VI) in this specific zone during water table fluctuation through laboratory experiment and numerical modeling. The higher reduction of Cr(VI) was found in the lower soil layer due to the lower Eh at the bottom layer of the unsaturated zone and the Cr(III) concentration increased with rise in water level and fluctuation amplitudes. After twice water fluctuation, nevertheless, there was still about 42.2% Cr retained in the soil and dominantly present as Cr(III) form. The model coupling reaction network with hydrodynamic field showed the cumulative Cr(III) in the unsaturated soil zone had a faster increase at the higher water level rise speed compared with lower rise speed. The cumulative Cr(VI) decreases over time in the saturated aquifers, whereas the cumulative Cr(III) increased with the increase of fluctuation amplitude. Reduction of Cr(VI) into Cr(III) was accompanied with Fe(II) and organic carbon oxidation. The results indicate that the hydrodynamic conditions have impacts on the redox environment of soil which could further affect the transformation and transport of Cr.